how can I align 10 fastq files and get the htseq-count on Mac

[nik12112]

Hello,

I have been strugelling to run Hisat2 code for alignment of several fastq files from human
I have read as many post as I could online and I went through the protocol here

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/

At the moment, i have the latest binary version of hisat2 in $HOME/bin
When I do hisat2 in the terminal and is shows that I don't import any input but it indicates that it is there and can be invoked

No index, query, or output file specified!
HISAT2 version 2.1.0 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)
Usage:


I have 10 fasta files on a folder named data on my desktop.
I have put the three scripts attached to the protocl in that folder and the files are shown below

NIHMS816842-supplement-README.txt
RNAseq_shell_script.sh
SRR1_1.fastq.gz SRR9_1.fastq.gz
SRR1_2.fastq.gz SRR9_2.fastq.gz
SRR2_1.fastq.gz SRR10_1.fastq.gz
SRR2_2.fastq.gz SRR10_2.fastq.gz
SRR3_1.fastq.gz
SRR3_2.fastq.gz
SRR4_1.fastq.gz
SRR4_2.fastq.gz
SRR5_1.fastq.gz
SRR5_2.fastq.gz
SRR6_1.fastq.gz
SRR6_2.fastq.gz
SRR7_1.fastq.gz
SRR7_2.fastq.gz rnaseq_ballgown.R
SRR8_1.fastq.gz rnaseq_pipeline.config.sh
SRR8_2.fastq.gz


Can you please let me know how I can run your code to align these fastq files with a Human gene reference ?

I did not change anything on any of the script which I believe that I must change the one in rnaseq_pipline.config.sh

At this moment, it is

NUMCPUS=8
HISAT2=$(which hisat2)
STRINGTIE=$(which stringtie)
SAMTOOLS=$(which samtools)
BASEDIR=$(pwd -P)/chrX_data
FASTQLOC="$BASEDIR/samples"
GENOMEIDX="$BASEDIR/indexes/chrX_tran"
GTFFILE="$BASEDIR/genes/chrX.gtf"
PHENODATA="$BASEDIR/geuvadis_phenodata.csv"
TEMPLOC="./tmp" #this will be relative to the output directory
reads1=(${FASTQLOC}/*_1.*)
reads1=("${reads1[@]##*/}")
reads2=("${reads1[@]/_1./_2.}")


All what I want is to get the htseq-count. txt files for each sample

I am looking forward to hearing from you
Best Regards,
Nik